From ngoto ¡÷ gen-info.osaka-u.ac.jp Tue Dec 29 04:45:20 2009 From: ngoto ¡÷ gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Tue, 29 Dec 2009 18:45:20 +0900 Subject: [BioRuby-ja] BioRuby 1.4.0 is released Message-ID: <20091229094520.D1C4B1CBC436@idnmail.gen-info.osaka-u.ac.jp> Hi all, We are pleased to announce the release of BioRuby 1.4.0. The archive is available at: http://bioruby.org/archive/bioruby-1.4.0.tar.gz Web page: http://bioruby.org/ http://bioruby.open-bio.org/ API documentation: http://bioruby.org/rdoc/ Bug report: http://rubyforge.org/projects/bioruby/ We also put RubyGems pacakge at RubyForge and Gemcutter. You can easily install by using RubyGems. First, check the version number by using search command: % gem search --remote bio and find "bio (1.4.0)" in the list. Then, % sudo gem install bio You can also obtain bioruby gem file from bioruby.org. http://bioruby.org/archive/gems/bio-1.4.0.gem Here is a brief summary of changes. = PhyloXML support Support for reading and writing PhyloXML file format is added, developed by Diana Jaunzeikare, mentored by Christian M Zmasek and co-mentors, supported by Google Summer of Code 2009 in collaboration with the National Evolutionary Synthesis Center (NESCent). = FASTQ file format support Support for reading and writing FASTQ file format is added. All of the three FASTQ format variants are supported. The code is written by Naohisa Goto, with the help of discussions in the open-bio-l mailing list. The prototype of Bio::Fastq class was first developed during the BioHackathon 2009 held in Okinawa. = DNA chromatogram support Support for reading DNA chromatogram files are added. SCF and ABIF file formats are supported. The code is developed by Anthony Underwood. = MEME (motif-based sequence analysis tools) support Support for running MAST (Motif Aliginment & Search Tool, part of the MEME Suite, motif-based sequence analysis tools) and parsing its results are added. The code is developed by Adam Kraut. = Improvement of KEGG parser classes Some new methods are added to parse new fields added to some KEGG file formats. Unit tests for KEGG parsers are also added and improved. = Many sample scripts are added Many sample scripts showing demonstrations of usages of classes are added. They were originally primitive test codes written in the "if __FILE__ == $0" convention. = Unit tests can test installed BioRuby Mechanism to load library and to find test data in the unit tests are changed, and target library path and test data path can be changed with environment variables. In addition, many changes have been made, including incompatible changes. For more information, see RELEASE_NOTES.rdoc and ChangeLog in the release archive or at: http://github.com/bioruby/bioruby/blob/1.4.0/RELEASE_NOTES.rdoc http://github.com/bioruby/bioruby/blob/1.4.0/ChangeLog Hope you enjoy. Naohisa Goto ngoto ¡÷ gen-info.osaka-u.ac.jp / ng ¡÷ bioruby.org From ngoto ¡÷ gen-info.osaka-u.ac.jp Tue Dec 29 09:45:20 2009 From: ngoto ¡÷ gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Tue, 29 Dec 2009 18:45:20 +0900 Subject: [BioRuby-ja] BioRuby 1.4.0 is released Message-ID: <20091229094520.D1C4B1CBC436@idnmail.gen-info.osaka-u.ac.jp> Hi all, We are pleased to announce the release of BioRuby 1.4.0. The archive is available at: http://bioruby.org/archive/bioruby-1.4.0.tar.gz Web page: http://bioruby.org/ http://bioruby.open-bio.org/ API documentation: http://bioruby.org/rdoc/ Bug report: http://rubyforge.org/projects/bioruby/ We also put RubyGems pacakge at RubyForge and Gemcutter. You can easily install by using RubyGems. First, check the version number by using search command: % gem search --remote bio and find "bio (1.4.0)" in the list. Then, % sudo gem install bio You can also obtain bioruby gem file from bioruby.org. http://bioruby.org/archive/gems/bio-1.4.0.gem Here is a brief summary of changes. = PhyloXML support Support for reading and writing PhyloXML file format is added, developed by Diana Jaunzeikare, mentored by Christian M Zmasek and co-mentors, supported by Google Summer of Code 2009 in collaboration with the National Evolutionary Synthesis Center (NESCent). = FASTQ file format support Support for reading and writing FASTQ file format is added. All of the three FASTQ format variants are supported. The code is written by Naohisa Goto, with the help of discussions in the open-bio-l mailing list. The prototype of Bio::Fastq class was first developed during the BioHackathon 2009 held in Okinawa. = DNA chromatogram support Support for reading DNA chromatogram files are added. SCF and ABIF file formats are supported. The code is developed by Anthony Underwood. = MEME (motif-based sequence analysis tools) support Support for running MAST (Motif Aliginment & Search Tool, part of the MEME Suite, motif-based sequence analysis tools) and parsing its results are added. The code is developed by Adam Kraut. = Improvement of KEGG parser classes Some new methods are added to parse new fields added to some KEGG file formats. Unit tests for KEGG parsers are also added and improved. = Many sample scripts are added Many sample scripts showing demonstrations of usages of classes are added. They were originally primitive test codes written in the "if __FILE__ == $0" convention. = Unit tests can test installed BioRuby Mechanism to load library and to find test data in the unit tests are changed, and target library path and test data path can be changed with environment variables. In addition, many changes have been made, including incompatible changes. For more information, see RELEASE_NOTES.rdoc and ChangeLog in the release archive or at: http://github.com/bioruby/bioruby/blob/1.4.0/RELEASE_NOTES.rdoc http://github.com/bioruby/bioruby/blob/1.4.0/ChangeLog Hope you enjoy. Naohisa Goto ngoto ¡÷ gen-info.osaka-u.ac.jp / ng ¡÷ bioruby.org